Patch Clamp Analysis

matlab scripts for analyzing and plotting patch clamp data

Overview

This script takes the electrophysiology data from whole cell patch clamp experiments that has been saved to multiple worksheets of an excel spreadsheet file and pretty plots the results according to the type of experiment that was performed. There are 4 kinds of experiments possible:

1. epsc: the spontaneous membrane voltage of the neuron was recorded for 60 seconds, no current or voltage was injected
2. I-clamp: increasing steps of current were injected into the neuron to elicit action potentials
3. IV plot: increasing voltage steps were injected into the neuron to elicit changes in current, the magnitude of the current response to voltage step is used to generate an I-V plot of voltage-gated sodium currents, voltage-gated fast potassium currents, and voltage-gated slow potassium currents.
4. ntx: the spontaneous membrane voltage of the neuron was recorded in response to the application of various neurmodulatory agents, informatiton about the timing and type of drug application is contained in the labels.xlsx file in this repository.

Running the script

Before running the script, specify the location of the excel spreadsheets containing the data and drug injection labels (if applicable) as the variable path. Once initialized, the script will prompt the user to specify which worksheet they want to analyze, and the worksheet that the drug injection labels are located in (if applicable).

page of worksheet? 

If the identified experimental type is epsc, the program will plot the spontaneous activity and then prompt the user to alter the y range if necessary:

Y limit range

This plot is fairly zoomed in on the data, so in order to fix the scaling to cover a range of ~500mV, select a range closer to [-180 320]

This is a pretty good looking range, so we agree to keep it

ok? (y=1, n=0): 1

You also have the option to change the title of the plot, if so desired. Or to skip this step, simply click return

change title? (leave blank to keep it the same)

And then, save the output figure into the directory specified by path

save? (y=1, n=0) 

If the identified data type is I-clamp, the program will plot the full current clamp trace and allow the user to change the plot title and save the result:

If the identified data type is NTX, the program will prompt the user to specify which page of the labels spreadsheet contains the relevant tags:

page of label spreadhseet to use?: 1

The raw data the is plotted looks pretty ugly, so the program prompts the user to specify what range of x values to plot

range for data

The start point should be somewhere near the beginning of the actual recording:

The end point should be somewhere near the end of the recording:

So, we specify the program to plot within the range [11780 129500]

ok? (y=1, n=0): 1

And then fix the y range to cover approximately 500mV again

y limit range: [-220 250]

Finally, the program puts in the time points and labels for the different drug injections:

Finally, if the identified data type is IV, the program will generate a figure with 2 panels:

The top panel shows the raw data of all voltage clamp steps overlaid on top of each other, while the bottom panel shows the calculated IV plots for the sodium and fast and slow potassium currents.